Rapidly developing next-generation sequencing (NGS) technologies produce
a large amount of data across the whole human genome and allow a large
number of DNA samples to be analyzed simultaneously. Screening cell-free
fetal DNA (cffDNA) obtained from maternal blood using NGS technologies
has provided new opportunities for non-invasive prenatal diagnosis
(NIPD) of fetal aneuploidies. One of the major challenges to the
analysis of fetal abnormalities is the development of accurate and
reliable algorithms capable of analyzing large numbers of short sequence
reads. Several such algorithms have recently been developed. Here, we
provide a review of recent NGS-based NIPD methods as well as the
available algorithms for short-read sequence analysis. We furthermore
introduce the practical application of these algorithms for the
detection of different types of fetal aneuploidies, and compare the
performance, cost and complexity of each approach for clinical
deployment. Our review identifies several main technologies and trends
in NGS-based NIPD. The main considerations for clinical development for
NIPD and screening tests using DNA sequencing are: accuracy,
intellectual property, cost and the ability to screen for a wide range
of chromosomal abnormalities and genetic defects. The cost of the
diagnostic test depends on the sequencing method, diagnostic algorithm
and volume of the tests. If the cost of sequencing equipment and
reagents remains at or around current levels, targeted approaches for
sequencing-based aneuploidy testing and SNP-based methods are preferred.

Conclusion:

Since the discovery of the cell-free fetal nucleic acid sequences in
maternal peripheral blood, several methods for highly accurate and
highly sensitive aneuploidy testing using NGS technology either for full
genome sequencing or sequencing of targeted areas of the genome were
developed. Prenatal tests utilizing these methods are already offered as
screening tests for trisomy 21, 18 and 13, reducing the need for risky
invasive procedures. Additional clinical trials are underway to validate
these methods for use as diagnostic tests for both high-risk
pregnancies and screening of the general population. The final decision
on the implementation of a NGS-based test for NIPD of aneuploidy in
clinical practice should be based on the criteria of high diagnostic
accuracy, clinical and cost-effectiveness and the ability to make a
diagnosis even in cases where the content of cffDNA is low. Furthermore,
large-scale validation studies should be carried out independent from
the tests’ manufacturing companies. Tests implemented in a clinical
setting should not be time consuming, which is very important in
prenatal diagnosis. It is also important to take into account the
nationality of the patients in order to implement the test in clinics
around the world. Tests should also require a minimal cost of equipment
and infrastructure in order to be available to small laboratories around
the world. Today NGS-based tests for diagnosis of trisomies 21, 18 and
13 may be combined with ultrasonographic detection and serum markers for
more accurate diagnosis of fetal aneuploidy, in order to avoid invasive
procedures. Methods utilizing full genome sequencing allow for accurate
detection of other autosomal and sex aneuploidies, but are limited by
the high cost of sequencing. Sequencing of targeted areas of the genome
allows one to significantly lower the cost of sequencing while providing
high accuracy and sensitivity in diagnosing common aneuploidies.
Methods utilizing parental genotypes, where DNA from one or both parents
is available, in addition to common trisomy detection, provide for
highly accurate counts of autosomes and sex chromosomes and can be
performed using significantly cheaper and easier to operate sequencing
equipment. Our review demonstrated that NGS-based NIPD is a rapidly
evolving field with many research teams developing and commercializing
tests using new technologies and performing large scale clinical trials.
As the new NGS technologies become available, new methods for NIPD will
be developed that allow the analysis of a broader spectrum of
chromosomal abnormalities and genetic diseases, and cost will be
reduced. Several commercial NIPD providers developed proprietary fetal
quantifiers and protocols for increasing diagnostic accuracy of the
tests and these may not be publicly available. All of the reviewed
methods bear equipment, technology, cost, intellectual property and
performance risk; thus, careful consideration should be given to each of
these aspects when deploying or developing NGS-based NIPD in a clinical
setting.

Sequencing requirements (see table 2 in the paper for Verinata, Ariosa and Sequenom):

Monday, March 14, 2011

One interesting resource for biomedical research - Aging Research Portfolio shows how much is being spent on various research projects worldwide. Today we tried searching for "Amniocentesis" using its advanced search feature and found that over 90 million dollars were spent by various organizations on that invasive procedure. What would be interesting to see is how much is spent on the Non-invasive prenatal diagnostics.

One interesting project is was "Chorionic villus sampling vs amniocentesis-data center" here is a screenshot:

Thursday, February 10, 2011

Eureka! Alliluia!
Those now if you are in your 40s and get pregnant sometime closer to the end of the year, most likely you won't need to go for the amniocentesis. Sequenom just confirmed that their non-invasive T21 test is just as accurate as the amnio, but without side effects!
Unfortunately, the company's marketing and PR department is the complete opposite of their R&D. The only mention of the test accuracy data is in their brief press release below off PR Newswire. We did not pick it up from WSJ, Bloomberg or Forbes journalists. Their CEO or CMO is not on the air or on TV. And it seems like we are the only blog covering this historic event!

SAN DIEGO, Feb. 10, 2011 /PRNewswire/ -- Sequenom (Nasdaq:SQNM - News) is very pleased to announce publication in the American Journal of Obstetrics and Gynecology (doi: 10.1016/j.ajog.2010.12.060) of Sequenom CMM's "locked assay" study.

The paper entitled "Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting" is available through the 'Articles Online First' section of the American Journal of Obstetrics and Gynecology website – http://www.ajog.org. The article is scheduled to appear in the March issue of the journal to be published both online and in print.

Study Results

The performance of a massively parallel shotgun sequencing based assay for noninvasive detection of fetal aneuploidy was evaluated on a set of 480 plasma samples from pregnant women at high-risk for fetal chromosomal aneuploidy. Utilizing 449 samples, all 39 trisomy 21 (T21) samples were correctly identified, while one of the 410 euploid samples was misclassified as T21. The overall classification showed 100% sensitivity (95% CI: 89% to 100%) and 99.7 specificity (95% CI: 98.5% to 99%). A total of 31 samples were removed due to insufficient quantity, breakage or failing pre-specified quality control criteria.

"This important study demonstrated that massively parallel shotgun sequencing is a potentially viable path for noninvasive prenatal diagnosis of fetal Trisomy 21 and warrants its validation in a larger clinical validation study," said Harry F. Hixson, Jr. PhD, chairman and chief executive officer of Sequenom. "We are very pleased with the results from the 'locked assay' study and are looking forward to the completion of the larger clinical validation study later this year."

Sequenom Center for Molecular Medicine (Sequenom CMM) initiated its pivotal clinical validation study in late December 2010. This validation study is designed to evaluate the clinical performance of the SensiGene T21 Laboratory Developed Test (LDT) for the detection of an overabundance of chromosome 21 in maternal blood, which is associated with fetal chromosome 21 aneuploidy. Testing of the clinical specimens is being performed at the Sequenom CMM CLIA-certified facility in San Diego.

About Sequenom Center for Molecular Medicine

Sequenom Center for Molecular Medicine (Sequenom CMM®) is a CAP accredited and CLIA-certified specialty reference laboratory dedicated to the development and commercialization of laboratory-developed genetic testing services for prenatal and eye conditions. Utilizing innovative proprietary technologies, Sequenom CMM provides test results that can be used as tools by clinicians in managing patient care. Testing services are available only upon request to physicians. Sequenom CMM works closely with key opinion leaders and experts in obstetrics, retinal care and genetics. The scientists use a variety of sophisticated and cutting-edge methodologies in the development and validation of tests. Sequenom CMM is changing the landscape in genetic diagnostics. Visit http://www.scmmlab.com for more information on laboratory services.

Friday, January 28, 2011

The proof of concept of the test, which will be brought to market to market by the San Diego-based company Sequenom, Inc (NASDAQ: SQNM) sometime this year showed very high accuracy in a reasonably large clinical trial. We salute Dennis Lo and Sequenom on these results and hope that the tests will be launched to general public as soon as possible.
Now that we know that the test works, Sequenom has a moral duty to the pregnant women to bring it to market as soon as possible and reduce the number of unnecessary invasive procedures and resulting spontaneous abortions and damage to the fetus.

Here is a link to the story and Sequenom's press release
http://finance.yahoo.com/news/Professor-Dennis-Lo-Trisomy-prnews-709814539.html?x=0&.v=1

SAN DIEGO, Jan. 12, 2011 /PRNewswire/ -- Sequenom (Nasdaq:SQNM - News) is very pleased to note the publication in the British Medical Journal (BMJ 2011;342:c7401) of a groundbreaking international study led by our longstanding collaborator, Professor Dennis Lo of The Chinese University of Hong Kong. Building on early work from the Lo laboratory, the present paper is the first report of a large-scale clinical study that validates a noninvasive, plasma DNA-based approach for prenatally detecting Down's syndrome (T21). Sequenom congratulates the research team for their achievements.

(Logo: http://photos.prnewswire.com/prnh/20040415/SQNMLOGO)

About Sequenom

Sequenom, Inc. (NASDAQ:SQNM - News) is a life sciences company committed to improving healthcare through revolutionary genetic analysis solutions. Sequenom develops innovative technology, products and diagnostic tests that target and serve discovery and clinical research, and molecular diagnostics markets. The company was founded in 1994 and is headquartered in San Diego, California. Sequenom maintains a Web site at http://www.sequenom.com to which Sequenom regularly posts copies of its press releases as well as additional information about Sequenom. Interested persons can subscribe on the Sequenom Web site to email alerts or RSS feeds that are sent automatically when Sequenom issues press releases, files its reports with the Securities and Exchange Commission or posts certain other information to the Web site.

31st Annual Meeting
The Pregnancy MeetingTM
Date: February 7, 2011 - February 12, 2011
Location: Hilton San Francisco Union Square
333 O'Farrell St.
San Francisco, CA
415-771-1400
Use Group Code: SFM to get the special SMFM rate. Use the link below for online reservations.
www.HILTON.com
Description: The SMFM 31st Annual Meeting will present cutting-edge basic, clinical, and epidemiological research. In addition to oral and poster presentations, attendees will hear from world-renowned leaders in the specialty of maternal-fetal medicine.
Attachments: 2011 Exhibitor Prospectus
EXHIBIT SPACE for the SMFM 2011 ANNUAL MEETING is SOLD OUT.

31st Annual Meeting Preliminary Program
Click on the link above to download a PDF of the meeting brochure.